Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Indolyne experimental and computational studies: synthetic applications and origins of selectivities of nucleophilic additions.

ABSTRACT: Efficient syntheses of 4,5-, 5,6-, and 6,7-indolyne precursors beginning from commercially available hydroxyindole derivatives are reported. The synthetic routes are versatile and allow access to indolyne precursors that remain unsubstituted on the pyrrole ring. Indolynes can be generated under mild fluoride-mediated conditions, trapped by a variety of nucleophilic reagents, and used to access a number of novel substituted indoles. Nucleophilic addition reactions to indolynes proceed with varying degrees of regioselectivity; distortion energies control regioselectivity and provide a simple model to predict the regioselectivity in the nucleophilic additions to indolynes and other unsymmetrical arynes. This model has led to the design of a substituted 4,5-indolyne that exhibits enhanced nucleophilic regioselectivity.

SUBMITTER: Im GY

PROVIDER: S-EPMC3075889 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Indolyne experimental and computational studies: synthetic applications and origins of selectivities of nucleophilic additions.

Im G-Yoon J GY Bronner Sarah M SM Goetz Adam E AE Paton Robert S RS Cheong Paul H-Y PH Houk K N KN Garg Neil K NK

Journal of the American Chemical Society 20101129 50

Efficient syntheses of 4,5-, 5,6-, and 6,7-indolyne precursors beginning from commercially available hydroxyindole derivatives are reported. The synthetic routes are versatile and allow access to indolyne precursors that remain unsubstituted on the pyrrole ring. Indolynes can be generated under mild fluoride-mediated conditions, trapped by a variety of nucleophilic reagents, and used to access a number of novel substituted indoles. Nucleophilic addition reactions to indolynes proceed with varyin ...[more]

PMID: 21114321

Similar Datasets

Origins of Optical Activity in an Oxo-Helicene: Experimental and Computational Studies.

Project description:Helicenes are known to provide extremely strong optical activity. Prediction of the properties of helicenes may facilitate their design and synthesis for analytical or materials sciences. On a model 7,12,17-trioxa[11]helicene molecule, experimental results from multiple spectroscopic techniques are analyzed on the basis of density functional theory (DFT) simulations to test computational methodology and analyze the origins of chirality. Infrared (IR), vibrational circular dichroism (VCD), electronic circular dichroism (ECD), magnetic circular dichroism (MCD), and Raman optical activity (ROA, computations only) spectra are compared. Large dissymmetry factors are predicted both for vibrational (ROA/Raman ∼ VCD/IR ∼ 10-3) and electronic (ECD/Abs ∼10-2) optical activity, which could be verified experimentally except for ROA. Largest VCD signals come from a strong vibrational coupling of the C-H in-plane and out-of-plane bending modes in stacked helicene rings. The sum-over-states (SOS) approach appeared convenient for simulation of MCD spectra. Our results demonstrated that selected computational methods can be successfully used for reliable modeling of spectral and chiroptical properties of large helicenes. In particular, they can be used for guiding rational design of strongly chiral chromophores.

| S-EPMC7841950 | biostudies-literature

Nucleophilic 1,4-additions for natural product discovery.

Project description:Natural products remain an important source of drug candidates, but the difficulties inherent to traditional isolation, coupled with unacceptably high rates of compound rediscovery, limit the pace of natural product detection. Here we describe a reactivity-based screening method to rapidly identify exported bacterial metabolites that contain dehydrated amino acids (i.e., carbonyl- or imine-activated alkenes), a common motif in several classes of natural products. Our strategy entails the use of a commercially available thiol, dithiothreitol, for the covalent labeling of activated alkenes by nucleophilic 1,4-addition. Modification is easily discerned by comparing mass spectra of reacted and unreacted cell surface extracts. When combined with bioinformatic analysis of putative natural product gene clusters, targeted screening and isolation can be performed on a prioritized list of strains. Moreover, known compounds are easily dereplicated, effectively eliminating superfluous isolation and characterization. As a proof of principle, this labeling method was used to identify known natural products belonging to the thiopeptide, lanthipeptide, and linaridin classes. Further, upon screening a panel of only 23 actinomycetes, we discovered and characterized a novel thiopeptide antibiotic, cyclothiazomycin C.

| S-EPMC4168802 | biostudies-literature

Rules of Nucleophilic Additions to Zigzag Nanographene Diones*.

Project description:Nucleophilic addition of carbon-centered nucleophiles to nanographene ketones represents a valuable late-stage method for the functionalization of zigzag nanographenes, but its use is rare in the chemical literature. Using two model systems, non-Kekulé triangulene-4,8-dione and Kekulé anthanthrone, we identify unexpected regioselectivities and uncover the rules that govern these reactions. Considering the large number of nanographene ketones that have been reported since the pioneering work of Eric Clar, this method enables synthesis and exploration of hitherto unknown functionalized nanographenes.

| S-EPMC8251702 | biostudies-literature

Computational and experimental studies of a cell-imprinted-based integrated microfluidic device for biomedical applications.

Project description:It has been proved that cell-imprinted substrates molded from template cells can be used for the re-culture of that cell while preserving its normal behavior or to differentiate the cultured stem cells into the template cell. In this study, a microfluidic device was presented to modify the previous irregular cell-imprinted substrate and increase imprinting efficiency by regular and objective cell culture. First, a cell-imprinted substrate from template cells was prepared using a microfluidic chip in a regular pattern. Another microfluidic chip with the same pattern was then aligned on the cell-imprinted substrate to create a chondrocyte-imprinted-based integrated microfluidic device. Computational fluid dynamics (CFD) simulations were used to obtain suitable conditions for injecting cells into the microfluidic chip before performing experimental evaluations. In this simulation, the effect of input flow rate, number per unit volume, and size of injected cells in two different chip sizes were examined on exerted shear stress and cell trajectories. This numerical simulation was first validated with experiments with cell lines. Finally, chondrocyte was used as template cell to evaluate the chondrogenic differentiation of adipose-derived mesenchymal stem cells (ADSCs) in the chondrocyte-imprinted-based integrated microfluidic device. ADSCs were positioned precisely on the chondrocyte patterns, and without using any chemical growth factor, their fibroblast-like morphology was modified to the spherical morphology of chondrocytes after 14 days of culture. Both immunostaining and gene expression analysis showed improvement in chondrogenic differentiation compared to traditional imprinting methods. This study demonstrated the effectiveness of cell-imprinted-based integrated microfluidic devices for biomedical applications.

| S-EPMC8190060 | biostudies-literature

Computational and Experimental Studies of ADP-Ribosylation.

Project description:The macrodomains are a multifunctional protein family that function as receptors and enzymes acting on poly(ADP-ribose), ADP-ribosylated proteins, and other metabolites of nicotinamide adenine dinucleotide (NAD+). Several new functions for macrodomains, such as nucleic acid binding and protein-protein interaction, have recently been identified in this family. Here, we discuss methods for the identification of new macrodomains in viruses and the prediction of their function. This is followed by the expression and purification of these proteins following overexpression in bacterial cells and confirmation of folding and function using biophysical methods.

| S-EPMC5526223 | biostudies-literature

Causation in a cascade: the origins of selectivities in intramolecular nitrone cycloadditions.

Project description:The factors controlling chemo-, regio-, and stereoselectivity in a cascade of reactions starting from a bis(cyanoalkenyl)oxime and proceeding via nitrone cycloadditions have been unraveled through a series of density functional theory calculations with several different functionals. Both kinetic and thermodynamic control of the reaction cascade are important, depending upon the conditions. Kinetic control was analyzed by the distortion/interaction model and found to be dictated by differences in distortions of the cycloaddends in the transition states. A new mechanism competing with that originally proposed in the application of these reactions to the histrionicotoxin synthesis was discovered in these studies.

| S-EPMC3413729 | biostudies-literature

Isothiourea-catalysed enantioselective pyrrolizine synthesis: synthetic and computational studies.

Project description:The catalytic enantioselective synthesis of a range of cis-pyrrolizine carboxylate derivatives with outstanding stereocontrol (14 examples, >95?:?5 dr, >98?:?2 er) through an isothiourea-catalyzed intramolecular Michael addition-lactonisation and ring-opening approach from the corresponding enone acid is reported. An optimised and straightforward three-step synthetic route to the enone acid starting materials from readily available pyrrole-2-carboxaldehydes is delineated, with benzotetramisole (5 mol%) proving the optimal catalyst for the enantioselective process. Ring-opening of the pyrrolizine dihydropyranone products with either MeOH or a range of amines leads to the desired products in excellent yield and enantioselectivity. Computation has been used to probe the factors leading to high stereocontrol, with the formation of the observed cis-steroisomer predicted to be kinetically and thermodynamically favoured.

| S-EPMC5314687 | biostudies-literature

Additions of Aldehyde-Derived Radicals and Nucleophilic N-Alkylindoles to Styrenes by Photoredox Catalysis.

Project description:The consecutive addition of acyl radicals and N-alkylindole nucleophiles to styrenes was established, as well as some additional radical-nucleophile combinations. Both aryl and aliphatic aldehydes give reasonable yields. The reaction proceeds best for α-substituted styrenes, effectively creating a quaternary all-carbon center. Some iridium-based photoredox systems are catalytically active; furthermore, a base is needed in this transformation. Radicals are formed by reductive perester cleavage and hydrogen atom transfer.

| S-EPMC7304929 | biostudies-literature

Fluorinated synthetic anion carriers: experimental and computational insights into transmembrane chloride transport.

Project description:A series of fluorinated tripodal tris-thioureas function as highly active anion transporters across lipid bilayers and cell membranes. Here, we investigate their mechanism of action using anion transport assays in cells and synthetic vesicles and molecular modelling of transporter-lipid interactions. When compared with non-fluorinated analogues, fluorinated compounds demonstrate a different mechanism of membrane transport because the free transporter cannot effectively diffuse through the membrane. As a result, in H+/Cl- cotransport assays, fluorinated transporters require the presence of oleic acid to form anionic oleate complexes for recycling of the transporter, whereas non-fluorinated analogues readily diffuse through the membrane as free transporters and show synergistic transport with the proton transporter gramicidin. Molecular dynamics simulations revealed markedly stronger transporter-lipid interactions for fluorinated compounds compared with non-fluorinated analogues and hence, higher energy barriers for fluorinated compounds to cross the membrane as free transporters. With use of appropriate proton transporters to ensure measurement of the correct rate-limiting steps, the transport rates determined in synthetic vesicle assays show excellent agreement with the anion transport rates determined in cell-based assays. We conclude that integration of computational and experimental methods provides a strategy to optimise transmembrane anion transporter design for biomedical applications.

| S-EPMC6381411 | biostudies-literature

Synthetic and Computational Studies on the Rhodium-Catalyzed Hydroamination of Aminoalkenes.

Project description:The influence of ligand structure on rhodium-catalyzed hydroamination has been evaluated for a series of phosphinoarene ligands. These catalysts have been evaluated in a set of catalytic intramolecular Markovnikov hydroamination reactions. The mechanism of hydroamination catalyzed by the rhodium(I) complexes in this study was examined computationally, and the turnover-limiting step was elucidated. These computational studies were extended to a series of theoretical hydroamination catalysts to compare the electronic effects of the ancillary ligand substituents. The relative energies of intermediates and transition states were compared to those of intermediates in the reaction catalyzed by the unsubstituted catalyst. The experimental difference in the reactivities of electron-rich and electron-poor catalysts was compared to the computational results, and it was found that the activity for the electron-poor catalysts predicted from the reaction barriers was overestimated. Thus, the analysis of the catalysts in this study was expanded to include the binding preference of each ligand, in comparison to that of the unsubstituted ligand. This information accounts for the disparity between observed reactivity and the calculated overall reaction barrier for electron-poor ligands. The ligand-binding preferences for new ligand structures were calculated, and ligands that were predicted to bind strongly to rhodium generated catalysts for the experimental catalytic reactions that were more reactive than those predicted to bind more weakly.

| S-EPMC5510900 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data